LAMMPS (2 Apr 2025 - Development - d4867ab55e-modified)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
  using 1 OpenMP thread(s) per MPI task
# GJ thermostat

units   	metal
atom_style      full

boundary 	p p p
read_data argon.lmp
Reading data file ...
  orthogonal box = (0 0 0) to (32.146 32.146 32.146)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  864 atoms
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0       
  special bond factors coul:  0        0        0       
     0 = max # of 1-2 neighbors
     0 = max # of 1-3 neighbors
     0 = max # of 1-4 neighbors
     1 = max # of special neighbors
  special bonds CPU = 0.002 seconds
  read_data CPU = 0.015 seconds
include ff-argon.lmp
#############################
#Atoms types - mass - charge#
#############################
#@ 1 atom types #!THIS LINE IS NECESSARY DON'T SPEND HOURS FINDING THAT OUT!#

variable Ar equal 1

#############
#Atom Masses#
#############

mass ${Ar}      39.903
mass 1      39.903

###########################
#Pair Potentials - Tersoff#
###########################

pair_style      lj/cubic
pair_coeff      * * 0.0102701 3.42


velocity all create 10 2357 mom yes dist gaussian
neighbor 1 bin

timestep 0.1

compute myKE all ke
compute myPE all pe

fix lang all gjf 10 10 1 26488

run 5000

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Your simulation uses code contributions which should be cited:

- GJ methods: doi:10.1080/00268976.2019.1662506

@Article{gronbech-jensen_complete_2020,
title = {Complete set of stochastic Verlet-type thermostats for correct Langevin simulations},
volume = {118},
number = {8},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1662506},
doi = {10.1080/00268976.2019.1662506},
journal = {Molecular Physics},
author = {Grønbech-Jensen, Niels},
year = {2020}
}

- GJ-I vhalf method: doi:10.1080/00268976.2019.1570369

@Article{jensen_accurate_2019,
title = {Accurate configurational and kinetic statistics in discrete-time Langevin systems},
volume = {117},
url = {https://www.tandfonline.com/doi/full/10.1080/00268976.2019.1570369},
doi = {10.1080/00268976.2019.1570369},
number = {18},
journal = {Molecular Physics},
author = {Jensen, Lucas Frese Grønbech and Grønbech-Jensen, Niels},
year = {2019}
}

CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE

Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 6.9407173
  ghost atom cutoff = 6.9407173
  binsize = 3.4703587, bins = 10 10 10
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cubic, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.427 | 6.427 | 6.427 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
         0   10            -56.207652      0             -55.092137      33.341103    
      5000   9.3726166     -55.076514      0             -54.030985      342.43571    
Loop time of 2.11818 on 4 procs for 5000 steps with 864 atoms

Performance: 20394.822 ns/day, 0.001 hours/ns, 2360.512 timesteps/s, 2.039 Matom-step/s
63.1% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.53987    | 0.54922    | 0.56044    |   1.2 | 25.93
Bond    | 0.00058281 | 0.00063674 | 0.00075153 |   0.0 |  0.03
Neigh   | 0.10821    | 0.10912    | 0.11017    |   0.2 |  5.15
Comm    | 0.96075    | 0.97484    | 0.98645    |   1.1 | 46.02
Output  | 0.00026318 | 0.00026575 | 0.00027192 |   0.0 |  0.01
Modify  | 0.26142    | 0.2634     | 0.26465    |   0.2 | 12.44
Other   |            | 0.2207     |            |       | 10.42

Nlocal:            216 ave         216 max         216 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost:         884.75 ave         885 max         884 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs:           4536 ave        4737 max        4335 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 18144
Ave neighs/atom = 21
Ave special neighs/atom = 0
Neighbor list builds = 273
Dangerous builds = 0

fix energies all ave/time 1 20000 20000 c_myKE c_myPE #file ave.out

thermo 2000
run 35000
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.428 | 6.428 | 6.428 Mbytes
   Step          Temp          E_pair         E_mol          TotEng         Press     
      5000   9.3726166     -55.076514      0             -54.030985      342.43571    
      6000   9.6911866     -55.129244      0             -54.048177      329.72537    
      8000   9.7296551     -55.101417      0             -54.016059      337.46595    
     10000   10.098808     -55.083292      0             -53.956755      343.4122     
     12000   10.114344     -55.090905      0             -53.962635      341.3438     
     14000   10.230012     -55.085051      0             -53.943878      342.45237    
     16000   9.5989709     -55.090733      0             -54.019954      339.07584    
     18000   10.016071     -55.030131      0             -53.912824      358.79514    
     20000   9.7197057     -55.104072      0             -54.019824      335.89619    
     22000   9.959647      -55.152019      0             -54.041005      323.05805    
     24000   10.075138     -55.115242      0             -53.991345      334.76239    
     26000   10.227192     -55.125275      0             -53.984416      332.10131    
     28000   10.177109     -55.107097      0             -53.971825      337.32979    
     30000   9.521036      -55.099011      0             -54.036925      337.10716    
     32000   10.265633     -55.077016      0             -53.93187       346.01018    
     34000   10.173978     -55.097068      0             -53.962146      339.63562    
     36000   9.6032778     -55.152202      0             -54.080942      321.61646    
     38000   9.8802995     -55.048407      0             -53.946245      351.82506    
     40000   10.372288     -55.087634      0             -53.93059       343.34304    
Loop time of 17.867 on 4 procs for 35000 steps with 864 atoms

Performance: 16925.013 ns/day, 0.001 hours/ns, 1958.914 timesteps/s, 1.693 Matom-step/s
65.3% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.0932     | 5.1683     | 5.2256     |   2.5 | 28.93
Bond    | 0.0044473  | 0.0048347  | 0.0058137  |   0.8 |  0.03
Neigh   | 0.85262    | 0.8601     | 0.87438    |   0.9 |  4.81
Comm    | 6.8164     | 6.8981     | 6.9859     |   2.6 | 38.61
Output  | 0.0046884  | 0.0047093  | 0.0047322  |   0.0 |  0.03
Modify  | 3.4107     | 3.4186     | 3.4248     |   0.3 | 19.13
Other   |            | 1.512      |            |       |  8.47

Nlocal:            216 ave         222 max         210 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:          905.5 ave         911 max         899 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs:        4535.75 ave        4837 max        4218 min
Histogram: 1 0 0 1 0 0 1 0 0 1

Total # of neighbors = 18143
Ave neighs/atom = 20.998843
Ave special neighs/atom = 0
Neighbor list builds = 2140
Dangerous builds = 0
Total wall time: 0:00:21
